Starting phenix.real_space_refine
on Sat May 17 12:37:07 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8jhf_36264/05_2025/8jhf_36264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jhf_36264/05_2025/8jhf_36264.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jhf_36264/05_2025/8jhf_36264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jhf_36264/05_2025/8jhf_36264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jhf_36264/05_2025/8jhf_36264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jhf_36264/05_2025/8jhf_36264.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1772 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     320      5.49       5
     S      35      5.16       5
     C    8219      2.51       5
     N    2739      2.21       5
     O    3389      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14703
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "K"
      Number of atoms: 2014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 2014
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 248}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "A"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 776
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 672
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "C"
      Number of atoms: 850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 850
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 3, 'TRANS': 108}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 693
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 825
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "H"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 740
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "I"
      Number of atoms: 3253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 3253
          Classifications: {'DNA': 160}
          Link IDs: {'rna3p': 159}
    Chain: "J"
      Number of atoms: 3307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 3307
          Classifications: {'DNA': 160}
          Link IDs: {'rna3p': 159}
    Chain: "K"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' ZN': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1726  SG  CYS K 319      83.531  34.352  85.709  1.00145.38           S
  ATOM   1741  SG  CYS K 321      84.756  36.893  84.198  1.00141.85           S
  ATOM   1766  SG  CYS K 324      86.241  36.603  85.599  1.00143.31           S

  Time building chain proxies: 8.19, per 1000 atoms: 0.56
  Number of scatterers: 14703
  At special positions: 0
  Unit cell: (110.4, 125.12, 142.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      35     16.00
     P     320     15.00
     O    3389      8.00
     N    2739      7.00
     C    8219      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.52
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 401 "
        pdb="ZN    ZN K 401 " - pdb=" SG  CYS K 319 "
        pdb="ZN    ZN K 401 " - pdb=" SG  CYS K 324 "
        pdb="ZN    ZN K 401 " - pdb=" SG  CYS K 321 "


  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      61.1% alpha, 2.3% beta
      141 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 6.12
  Creating SS restraints...
    Processing helix  chain 'K' and resid 77 through 94
      removed outlier: 3.560A  pdb=" N   ASP K  90 " --> pdb=" O   SER K  86 " (cutoff:3.500A)
      Proline residue:  K  91  - end of helix
    Processing helix  chain 'K' and resid 149 through 159
    Processing helix  chain 'K' and resid 160 through 170
    Processing helix  chain 'K' and resid 174 through 191
      removed outlier: 3.689A  pdb=" N   PHE K 189 " --> pdb=" O   TYR K 185 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 266 through 270
      removed outlier: 3.583A  pdb=" N   PHE K 270 " --> pdb=" O   PRO K 267 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 321 through 327
    Processing helix  chain 'K' and resid 354 through 360
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.511A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.790A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 113
      removed outlier: 4.037A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.679A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.109A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 18 through 23
      removed outlier: 3.705A  pdb=" N   ALA C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 38
    Processing helix  chain 'C' and resid 49 through 71
      removed outlier: 3.793A  pdb=" N   ASN C  71 " --> pdb=" O   GLU C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 77
    Processing helix  chain 'C' and resid 82 through 93
      removed outlier: 3.709A  pdb=" N   ASP C  93 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 100
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 53 through 81
      removed outlier: 3.558A  pdb=" N   GLY D  57 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.602A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 120
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.597A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.653A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.667A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 29
      removed outlier: 4.061A  pdb=" N   ILE F  26 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.053A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 18 through 23
    Processing helix  chain 'G' and resid 28 through 37
      removed outlier: 3.540A  pdb=" N   ILE G  32 " --> pdb=" O   PRO G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 49 through 76
    Processing helix  chain 'G' and resid 82 through 93
      removed outlier: 3.984A  pdb=" N   ASP G  93 " --> pdb=" O   ALA G  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 100
    Processing helix  chain 'G' and resid 114 through 119
      removed outlier: 3.919A  pdb=" N   ILE G 118 " --> pdb=" O   HIS G 114 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 119 through 124
      removed outlier: 3.837A  pdb=" N   GLN G 124 " --> pdb=" O   LYS G 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 53 through 81
      removed outlier: 3.678A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 98
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.563A  pdb=" N   THR H 119 " --> pdb=" O   VAL H 115 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   SER H 120 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA H 121 " --> pdb=" O   LYS H 117 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 230 through 234
      removed outlier: 4.324A  pdb=" N   ALA K 261 " --> pdb=" O   LEU K 234 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 281 through 282
    Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.904A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.590A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 46
      removed outlier: 6.556A  pdb=" N   ARG C  45 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.129A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 45 through 46
      removed outlier: 7.060A  pdb=" N   ARG G  45 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 80 through 81

    431 hydrogen bonds defined for protein.
    1263 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      365 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      141 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 5.50

  Time building geometry restraints manager: 4.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 3082
        1.33 -     1.45: 4823
        1.45 -     1.57: 7022
        1.57 -     1.69: 638
        1.69 -     1.81: 55
  Bond restraints: 15620
  Sorted by residual:
  bond pdb=" N   ASP G  93 "
       pdb=" CA  ASP G  93 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.19e-02 7.06e+03 9.17e+00
  bond pdb=" C2  SAM K 402 "
       pdb=" N3  SAM K 402 "
    ideal  model  delta    sigma   weight residual
    1.322  1.380 -0.058 2.00e-02 2.50e+03 8.43e+00
  bond pdb=" N   ASN K 221 "
       pdb=" CA  ASN K 221 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.21e-02 6.83e+03 8.37e+00
  bond pdb=" N   LYS K 219 "
       pdb=" CA  LYS K 219 "
    ideal  model  delta    sigma   weight residual
    1.452  1.492 -0.040 1.41e-02 5.03e+03 8.14e+00
  bond pdb=" N   GLU K 233 "
       pdb=" CA  GLU K 233 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.23e-02 6.61e+03 8.11e+00
  ... (remaining 15615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 22194
        2.27 -     4.55: 222
        4.55 -     6.82: 24
        6.82 -     9.10: 3
        9.10 -    11.37: 1
  Bond angle restraints: 22444
  Sorted by residual:
  angle pdb=" N   LEU G  96 "
        pdb=" CA  LEU G  96 "
        pdb=" C   LEU G  96 "
      ideal   model   delta    sigma   weight residual
     111.82  106.63    5.19 1.16e+00 7.43e-01 2.00e+01
  angle pdb=" C   LEU G  99 "
        pdb=" N   ILE G 100 "
        pdb=" CA  ILE G 100 "
      ideal   model   delta    sigma   weight residual
     121.80  115.96    5.84 1.40e+00 5.10e-01 1.74e+01
  angle pdb=" CA  LEU D  98 "
        pdb=" CB  LEU D  98 "
        pdb=" CG  LEU D  98 "
      ideal   model   delta    sigma   weight residual
     116.30  127.67  -11.37 3.50e+00 8.16e-02 1.06e+01
  angle pdb=" O   SAM K 402 "
        pdb=" C   SAM K 402 "
        pdb=" OXT SAM K 402 "
      ideal   model   delta    sigma   weight residual
     126.77  117.79    8.98 3.00e+00 1.11e-01 8.97e+00
  angle pdb=" CA  GLU G  95 "
        pdb=" C   GLU G  95 "
        pdb=" O   GLU G  95 "
      ideal   model   delta    sigma   weight residual
     120.82  117.69    3.13 1.05e+00 9.07e-01 8.91e+00
  ... (remaining 22439 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 7087
       35.97 -    71.94: 1452
       71.94 -   107.90: 24
      107.90 -   143.87: 1
      143.87 -   179.84: 5
  Dihedral angle restraints: 8569
    sinusoidal: 5598
      harmonic: 2971
  Sorted by residual:
  dihedral pdb=" C4'  DT J 138 "
           pdb=" C3'  DT J 138 "
           pdb=" O3'  DT J 138 "
           pdb=" P    DC J 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.84 -179.84     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA I 145 "
           pdb=" C3'  DA I 145 "
           pdb=" O3'  DA I 145 "
           pdb=" P    DT I 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   45.07  174.93     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT I  99 "
           pdb=" C3'  DT I  99 "
           pdb=" O3'  DT I  99 "
           pdb=" P    DA I 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   64.06  155.94     1      3.50e+01 8.16e-04 1.50e+01
  ... (remaining 8566 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1879
       0.035 -    0.069: 512
       0.069 -    0.104: 103
       0.104 -    0.138: 32
       0.138 -    0.173: 7
  Chirality restraints: 2533
  Sorted by residual:
  chirality pdb=" C2' SAM K 402 "
            pdb=" C1' SAM K 402 "
            pdb=" C3' SAM K 402 "
            pdb=" O2' SAM K 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.58   -0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CA  ASP D  48 "
            pdb=" N   ASP D  48 "
            pdb=" C   ASP D  48 "
            pdb=" CB  ASP D  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ASP E  81 "
            pdb=" N   ASP E  81 "
            pdb=" C   ASP E  81 "
            pdb=" CB  ASP E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.11e-01
  ... (remaining 2530 not shown)

  Planarity restraints: 1733
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE K 231 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   ILE K 231 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE K 231 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA K 232 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 264 "    0.013 2.00e-02 2.50e+03   1.45e-02 5.28e+00
        pdb=" CG  TRP K 264 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 264 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 264 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 264 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 264 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 264 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 264 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 264 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 264 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F  31 "   -0.030 5.00e-02 4.00e+02   4.53e-02 3.28e+00
        pdb=" N   PRO F  32 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO F  32 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO F  32 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1730 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 422
        2.67 -     3.23: 12731
        3.23 -     3.78: 25247
        3.78 -     4.34: 31782
        4.34 -     4.90: 46876
  Nonbonded interactions: 117058
  Sorted by model distance:
  nonbonded pdb=" O   THR K 284 "
            pdb=" OG1 THR K 288 "
     model   vdw
     2.111 3.040
  nonbonded pdb=" O   MET K 188 "
            pdb=" OG  SER K 193 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O2   DT I 157 "
            pdb=" N6   DA J  11 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG1 THR K  97 "
            pdb=" OD1 ASN K 208 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG1 THR K  97 "
            pdb=" O   ASN K 208 "
     model   vdw
     2.231 3.040
  ... (remaining 117053 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 41 through 134)
  selection = (chain 'E' and (resid 41 through 60 or (resid 61 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 62 through 134))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 19 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 16 through 124)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 28 through 72 or (resid 73 through 74 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 75 through 122))
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.090
  Set scattering table:                    0.140
  Process input model:                     39.980
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  15623  Z= 0.196
  Angle     :  0.613  11.372  22444  Z= 0.357
  Chirality :  0.035   0.173   2533
  Planarity :  0.004   0.045   1733
  Dihedral  : 27.225 179.840   6653
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  0.35 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.27), residues: 1007
  helix:  1.90 (0.22), residues: 598
  sheet: -0.18 (0.84), residues: 22
  loop : -2.15 (0.27), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP K 264 
 HIS   0.004   0.001   HIS K  98 
 PHE   0.010   0.001   PHE K 281 
 TYR   0.025   0.001   TYR F  88 
 ARG   0.008   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12945 (  796)
  hydrogen bonds       : angle       5.07210 ( 1993)
  metal coordination   : bond        0.00281 (    3)
  covalent geometry    : bond        0.00395 (15620)
  covalent geometry    : angle       0.61268 (22444)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 1.249 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7208 (pmm) cc_final: 0.6878 (pmm)
REVERT: E   76 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: G   95 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6652 (mm-30)
REVERT: G  115 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7519 (tptp)
  outliers start: 6
  outliers final: 0
  residues processed: 161
  average time/residue: 0.3137
  time to fit residues: 69.7516
Evaluate side-chains
  134 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 98 optimal weight:   40.0000
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 118 optimal weight:   10.0000
   overall best weight:    4.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
K 181 HIS
** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.135095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.088109 restraints weight = 34297.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.087891 restraints weight = 21814.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.088495 restraints weight = 15787.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  15623  Z= 0.220
  Angle     :  0.616   7.883  22444  Z= 0.360
  Chirality :  0.037   0.162   2533
  Planarity :  0.004   0.040   1733
  Dihedral  : 30.109 178.512   4658
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.66 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.27), residues: 1007
  helix:  2.06 (0.22), residues: 605
  sheet:  0.27 (0.88), residues: 22
  loop : -2.19 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP K 264 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.010   0.001   PHE K 281 
 TYR   0.022   0.002   TYR F  88 
 ARG   0.003   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06745 (  796)
  hydrogen bonds       : angle       3.51707 ( 1993)
  metal coordination   : bond        0.00363 (    3)
  covalent geometry    : bond        0.00497 (15620)
  covalent geometry    : angle       0.61605 (22444)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 1.239 
Fit side-chains
REVERT: K   98 HIS cc_start: 0.5329 (m90) cc_final: 0.5127 (m170)
REVERT: K  100 MET cc_start: 0.7128 (pmm) cc_final: 0.6399 (mmp)
REVERT: E   76 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8502 (tm-30)
REVERT: G  115 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7591 (tptp)
  outliers start: 11
  outliers final: 7
  residues processed: 151
  average time/residue: 0.3005
  time to fit residues: 63.8114
Evaluate side-chains
  141 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 92 optimal weight:    2.9990
   chunk 127 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0060
   chunk 35 optimal weight:    3.9990
   chunk 113 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 81 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 112 optimal weight:   20.0000
   overall best weight:    2.8004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
K 316 ASN
B  25 ASN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.136731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.090082 restraints weight = 34053.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.090136 restraints weight = 23058.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.090883 restraints weight = 15888.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15623  Z= 0.177
  Angle     :  0.565   6.584  22444  Z= 0.335
  Chirality :  0.035   0.156   2533
  Planarity :  0.004   0.043   1733
  Dihedral  : 30.069 179.217   4658
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.40 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.27), residues: 1007
  helix:  2.25 (0.22), residues: 607
  sheet:  0.30 (0.88), residues: 22
  loop : -2.16 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K 264 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.009   0.001   PHE H  62 
 TYR   0.020   0.001   TYR H  80 
 ARG   0.005   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05748 (  796)
  hydrogen bonds       : angle       3.27604 ( 1993)
  metal coordination   : bond        0.00266 (    3)
  covalent geometry    : bond        0.00388 (15620)
  covalent geometry    : angle       0.56516 (22444)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 1.106 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7132 (pmm) cc_final: 0.6412 (mmp)
REVERT: E   76 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8506 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 151
  average time/residue: 0.2870
  time to fit residues: 61.5653
Evaluate side-chains
  145 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain H residue  115 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 127 optimal weight:   10.0000
   chunk 52 optimal weight:    0.4980
   chunk 80 optimal weight:    6.9990
   chunk 60 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 121 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   overall best weight:    4.2988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.134615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.087524 restraints weight = 33770.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.087630 restraints weight = 21711.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.088407 restraints weight = 14804.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  15623  Z= 0.219
  Angle     :  0.605   7.051  22444  Z= 0.355
  Chirality :  0.036   0.156   2533
  Planarity :  0.004   0.044   1733
  Dihedral  : 30.148 179.708   4658
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.74 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.27), residues: 1007
  helix:  2.13 (0.22), residues: 605
  sheet: -0.15 (0.82), residues: 24
  loop : -2.26 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K 264 
 HIS   0.004   0.001   HIS H  46 
 PHE   0.010   0.001   PHE H  62 
 TYR   0.018   0.002   TYR H  80 
 ARG   0.006   0.000   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06748 (  796)
  hydrogen bonds       : angle       3.41675 ( 1993)
  metal coordination   : bond        0.00356 (    3)
  covalent geometry    : bond        0.00494 (15620)
  covalent geometry    : angle       0.60452 (22444)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 1.093 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7176 (pmm) cc_final: 0.6721 (pmm)
REVERT: K  188 MET cc_start: 0.7738 (tmm) cc_final: 0.7437 (tmm)
REVERT: E   76 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8481 (tm-30)
  outliers start: 19
  outliers final: 15
  residues processed: 157
  average time/residue: 0.3043
  time to fit residues: 68.1125
Evaluate side-chains
  152 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 1.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  282 VAL
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain H residue  115 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 111 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    2.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.133837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.086542 restraints weight = 35397.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.086978 restraints weight = 21663.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.087727 restraints weight = 15009.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15623  Z= 0.174
  Angle     :  0.562   6.373  22444  Z= 0.333
  Chirality :  0.035   0.158   2533
  Planarity :  0.004   0.046   1733
  Dihedral  : 30.091 179.485   4658
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.98 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.27), residues: 1007
  helix:  2.26 (0.22), residues: 606
  sheet: -0.11 (0.89), residues: 22
  loop : -2.24 (0.28), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K 264 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.007   0.001   PHE H  62 
 TYR   0.014   0.001   TYR H  80 
 ARG   0.005   0.000   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05686 (  796)
  hydrogen bonds       : angle       3.19834 ( 1993)
  metal coordination   : bond        0.00235 (    3)
  covalent geometry    : bond        0.00383 (15620)
  covalent geometry    : angle       0.56165 (22444)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 1.070 
Fit side-chains
REVERT: K  100 MET cc_start: 0.6951 (pmm) cc_final: 0.6379 (mmp)
REVERT: K  188 MET cc_start: 0.7700 (tmm) cc_final: 0.7430 (tmm)
REVERT: K  241 MET cc_start: 0.7579 (tmm) cc_final: 0.6931 (tmm)
REVERT: E   76 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8460 (tm-30)
REVERT: G   95 GLU cc_start: 0.7798 (mp0) cc_final: 0.7561 (mp0)
  outliers start: 21
  outliers final: 16
  residues processed: 155
  average time/residue: 0.2849
  time to fit residues: 63.0001
Evaluate side-chains
  147 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  282 VAL
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain H residue  115 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0370
   chunk 78 optimal weight:    7.9990
   chunk 99 optimal weight:   20.0000
   chunk 34 optimal weight:    4.9990
   chunk 120 optimal weight:   10.0000
   chunk 89 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.9864

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.134663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.088768 restraints weight = 35401.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.088561 restraints weight = 22431.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.089164 restraints weight = 16252.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15623  Z= 0.157
  Angle     :  0.550   8.449  22444  Z= 0.326
  Chirality :  0.034   0.160   2533
  Planarity :  0.004   0.049   1733
  Dihedral  : 30.075 179.776   4658
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.10 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.27), residues: 1007
  helix:  2.40 (0.22), residues: 606
  sheet: -0.49 (0.96), residues: 24
  loop : -2.21 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K 264 
 HIS   0.007   0.001   HIS H  79 
 PHE   0.007   0.001   PHE H  62 
 TYR   0.025   0.001   TYR F  88 
 ARG   0.006   0.000   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05150 (  796)
  hydrogen bonds       : angle       3.05911 ( 1993)
  metal coordination   : bond        0.00171 (    3)
  covalent geometry    : bond        0.00339 (15620)
  covalent geometry    : angle       0.54978 (22444)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 1.164 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7020 (pmm) cc_final: 0.6380 (mmp)
REVERT: K  188 MET cc_start: 0.7859 (tmm) cc_final: 0.7624 (tmm)
REVERT: C   77 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8157 (mmtm)
REVERT: E   76 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8443 (tm-30)
  outliers start: 21
  outliers final: 13
  residues processed: 158
  average time/residue: 0.2740
  time to fit residues: 62.1177
Evaluate side-chains
  158 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  282 VAL
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0040
   chunk 5 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 80 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 98 optimal weight:   40.0000
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.7596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.135169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.088883 restraints weight = 35611.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.089130 restraints weight = 24456.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.089515 restraints weight = 16333.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15623  Z= 0.151
  Angle     :  0.538   5.501  22444  Z= 0.320
  Chirality :  0.033   0.156   2533
  Planarity :  0.004   0.051   1733
  Dihedral  : 30.065 179.343   4658
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 18.15 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.27), residues: 1007
  helix:  2.47 (0.22), residues: 606
  sheet: -0.48 (0.97), residues: 24
  loop : -2.16 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K 264 
 HIS   0.003   0.001   HIS K  98 
 PHE   0.007   0.001   PHE H  62 
 TYR   0.022   0.001   TYR H  80 
 ARG   0.006   0.000   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  796)
  hydrogen bonds       : angle       2.96943 ( 1993)
  metal coordination   : bond        0.00133 (    3)
  covalent geometry    : bond        0.00323 (15620)
  covalent geometry    : angle       0.53786 (22444)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 1.097 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7101 (pmm) cc_final: 0.6651 (pmm)
REVERT: C   77 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8188 (mmtm)
REVERT: E   76 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: G   95 GLU cc_start: 0.7657 (mp0) cc_final: 0.7160 (mp0)
REVERT: H  102 GLU cc_start: 0.6865 (pm20) cc_final: 0.6361 (pm20)
  outliers start: 16
  outliers final: 14
  residues processed: 158
  average time/residue: 0.2810
  time to fit residues: 63.2160
Evaluate side-chains
  157 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  282 VAL
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 89 optimal weight:    5.9990
   chunk 116 optimal weight:   20.0000
   chunk 74 optimal weight:    5.9990
   chunk 111 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 7 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 104 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  60 ASN
E 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.131430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.084077 restraints weight = 35436.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.083171 restraints weight = 20740.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.084009 restraints weight = 16266.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  15623  Z= 0.260
  Angle     :  0.638   8.988  22444  Z= 0.370
  Chirality :  0.038   0.158   2533
  Planarity :  0.004   0.044   1733
  Dihedral  : 30.262 179.902   4658
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.62 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.27), residues: 1007
  helix:  2.11 (0.21), residues: 605
  sheet: -0.72 (0.95), residues: 24
  loop : -2.30 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP K 264 
 HIS   0.006   0.001   HIS D  79 
 PHE   0.010   0.001   PHE D  62 
 TYR   0.044   0.002   TYR F  88 
 ARG   0.005   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07270 (  796)
  hydrogen bonds       : angle       3.48697 ( 1993)
  metal coordination   : bond        0.00523 (    3)
  covalent geometry    : bond        0.00597 (15620)
  covalent geometry    : angle       0.63809 (22444)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 1.080 
Fit side-chains
REVERT: K  100 MET cc_start: 0.6984 (pmm) cc_final: 0.6438 (pmm)
REVERT: E   76 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8475 (tm-30)
  outliers start: 20
  outliers final: 15
  residues processed: 152
  average time/residue: 0.3053
  time to fit residues: 66.1618
Evaluate side-chains
  146 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  282 VAL
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 83 optimal weight:    0.6980
   chunk 61 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
K 169 ASN
B  25 ASN
E 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.134838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.087706 restraints weight = 35445.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.087822 restraints weight = 21630.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.088636 restraints weight = 15150.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15623  Z= 0.154
  Angle     :  0.556   5.665  22444  Z= 0.330
  Chirality :  0.034   0.156   2533
  Planarity :  0.004   0.053   1733
  Dihedral  : 30.120 178.710   4658
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 19.56 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.27), residues: 1007
  helix:  2.35 (0.21), residues: 611
  sheet: -0.68 (0.94), residues: 24
  loop : -2.24 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K 264 
 HIS   0.004   0.001   HIS K  98 
 PHE   0.005   0.001   PHE E  84 
 TYR   0.053   0.001   TYR F  88 
 ARG   0.008   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 (  796)
  hydrogen bonds       : angle       3.01291 ( 1993)
  metal coordination   : bond        0.00128 (    3)
  covalent geometry    : bond        0.00328 (15620)
  covalent geometry    : angle       0.55602 (22444)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 1.099 
Fit side-chains
REVERT: K  188 MET cc_start: 0.7813 (tmm) cc_final: 0.7585 (tmm)
REVERT: C   77 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8180 (mmtm)
REVERT: E   76 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8453 (tm-30)
  outliers start: 15
  outliers final: 13
  residues processed: 155
  average time/residue: 0.2808
  time to fit residues: 61.9593
Evaluate side-chains
  151 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:   20.0000
   chunk 94 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 114 optimal weight:   40.0000
   chunk 82 optimal weight:    1.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.133609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.085350 restraints weight = 35514.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.086082 restraints weight = 21062.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.086895 restraints weight = 14959.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15623  Z= 0.180
  Angle     :  0.584  10.402  22444  Z= 0.341
  Chirality :  0.035   0.157   2533
  Planarity :  0.004   0.049   1733
  Dihedral  : 30.180 178.587   4658
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.79 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.27), residues: 1007
  helix:  2.36 (0.21), residues: 605
  sheet: -0.55 (0.96), residues: 24
  loop : -2.25 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K 264 
 HIS   0.004   0.001   HIS K  98 
 PHE   0.008   0.001   PHE H  62 
 TYR   0.053   0.001   TYR F  88 
 ARG   0.006   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05685 (  796)
  hydrogen bonds       : angle       3.12217 ( 1993)
  metal coordination   : bond        0.00253 (    3)
  covalent geometry    : bond        0.00400 (15620)
  covalent geometry    : angle       0.58383 (22444)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: K  188 MET cc_start: 0.7759 (tmm) cc_final: 0.7547 (tmm)
REVERT: C   77 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8198 (mmtm)
REVERT: E   76 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8455 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 152
  average time/residue: 0.2845
  time to fit residues: 61.4076
Evaluate side-chains
  150 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 15 optimal weight:    0.0270
   chunk 48 optimal weight:    8.9990
   chunk 8 optimal weight:   20.0000
   chunk 0 optimal weight:   40.0000
   chunk 50 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 120 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   overall best weight:    3.0046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.133772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.086149 restraints weight = 35127.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.086659 restraints weight = 21829.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.087180 restraints weight = 15260.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15623  Z= 0.180
  Angle     :  0.585  12.334  22444  Z= 0.341
  Chirality :  0.035   0.156   2533
  Planarity :  0.004   0.048   1733
  Dihedral  : 30.177 178.499   4658
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.79 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.27), residues: 1007
  helix:  2.33 (0.21), residues: 605
  sheet: -0.55 (0.96), residues: 24
  loop : -2.27 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K 264 
 HIS   0.005   0.001   HIS K  98 
 PHE   0.007   0.001   PHE H  62 
 TYR   0.065   0.002   TYR F  88 
 ARG   0.006   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05684 (  796)
  hydrogen bonds       : angle       3.11875 ( 1993)
  metal coordination   : bond        0.00259 (    3)
  covalent geometry    : bond        0.00400 (15620)
  covalent geometry    : angle       0.58487 (22444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3914.74 seconds
wall clock time: 69 minutes 16.85 seconds (4156.85 seconds total)